Posted
by
Roblimo
on Wednesday February 09, 2011 @07:52AM
from the hoping-to-make-viral-videos-before-long dept.

Zothecula writes "In a paper published in the current edition of Nature, an international team of scientists describe how they obtained the world's first single-shot images of intact viruses – a technology that could ultimately lead to moving video of molecules, viruses and live microbes. Another paper by the same team describes how they were also able to successfully utilize a new shortcut for determining the 3D structures of proteins. Both advances were achieved using the world's first hard X-ray free-electron laser – the Linac Coherent Light Source (LCLS) – which scientists hope could revolutionize the study of life."

While a movie of bursting viruses might be interesting, it won't be as scientifically useful as a movie of a virus that is (mostly) unaffected by having the movie taken of it.

This sort of stuff is like determining where a basketball is by throwing tennis balls at it and seeing where they land. You can only throw a few before the basketball becomes so affected by the tennis balls that you don't know where it is anymore (or how fast it's moving)...

I'm sure it would be possible to create an algorithm that could determine the path (ie velocity and speed at any point) the basketball has taken after a couple of positive hits by the tennis balls, if you know the exact initial velocity of the tennis balls, how long they take to land, and where they've landed. The first hit will affect the path of the ball, but you could account for that too. Unless you're also having to deal with other factors of course, like invisible obstacles or changing winds, though w

not the right analogy. It's as if you threw 1000000 BB's at a cement truck and everyonce in a while, all 1000000 BB's will strike the truck at the right angle to bounce off and make an image. They send large numbers of cement trucks through the BB beam to get even one image, so it's not some math trick as much as "who cares what happens to the virus after you've already bounced all the BB's off of it [at once]".

The duration of its individual pulses is incredibly short – a few millionths of a billionth of a second. That’s still long enough to cause its subjects to vaporize, but that doesn’t happen until after their pictures have been snapped.

You mean "normal" X-rays which is defined as the electromagnetic spectrum between 10 and 10,000 pm? As opposed to the backscatter X-rays which could range anywhere in the electromagnetic spectrum between 10 and 10,000 pm? Attenuation (transmission) and backscatter are different techniques for X-ray imaging - but they both still use X-rays. It's like the difference of looking at a stain glass window from the inside or the outside of the church - in both cases it's sunlight that does the illumination.

It does get more complicated when you talk about specific wavelength, intensity, and etc... when you try to measure dosage. But all X-ray methods utilize ionizing radiation which is carcinogenic. Dose may be a very small portion of what you get every day, or in the case of the X-ray laser here, it may be enough to vaporize you.

We see no measurable sample deterioration. With the X-ray pulses used in this study, the explosion of micrometre-sized objects is hydrodynamic and the sample burns from the outside inwards, rarefying and destroying outer contours first. Trapped electrons move inwards to neutralize an increasingly positive core, and leave behind a positively charged outer layer, which then peels off over some picoseconds.

No, they are destroyed. The X-ray pulse is short enough (10s of femtoseconds) that an image is collected before the virus (or other target) has time to explode. This is the big advantage of the LCLS over conventional X-ray sources.

"hard X-ray free-electron laser" - are the viruses realy intact after such a burst?

BFD.There's nothing like re-inventing the wheel. Royal R. Rife invented a non-lethal microscope [navi.net] way back in the 30's. However, just like Tesla, Farnsworth, Reich; Rife was ostracized by the peer community (read the corrupt medical and pharmaceutical organizations).

First of all, the picture of the mimivirus, this huge honking virus, is a black dot surrounded by a psychedelic laser field herngh gnarly. But that's the best picture they can get of the largest virus known to mankind? A Grateful Dead poster?

That's the diffraction pattern. The paper has more meaningful images after "iterative phase retrieval with the Hawk software package". Hawk is open source, apparently:

I am a physicist-in-training (grad student), and when I first heard of "free electron lasers" I was extremely impressed, because getting electrons into a multi-keV energy state that can lase without atoms involved sounded nearly impossible. Turns out it is, because these are not actually "lasers" the sense of Light Amplification by Stimulated Emission of Radiation. There is no population inversion [wikipedia.org] as in real lasers.

The name of this specific FEL, the "Linac Coherent Light Source", is a much more correct name. They shoot electrons through a wiggler, and as they wiggle they emit coherent photons. Coherency is they key property of laser light, but the name refers to the method of light creation more than the actual output. I don't know why the x-ray community has felt the need to use this misleading name.

Not only that, a Free electron laser (FEL) is only spatially coherent, not temporally coherent. This is a drawback of the "single-pass" method of X-Ray generation in FELs. Essentially, you can compare a FEL to amplified spontaneous emission (ASE) that is common in devices like superluminescent diodes. The bunching of electrons in FELs along the wiggler leads to different bunches that emit temporally coherent X-Rays, but across the entire FEL there are a large number of such bunches resulting in a spectral o

Because the word "laser" has taken on a broader meaning since it was coined, so that it is used to refer generically to any coherent electromagnetic wave generating device or phenomena. Laser is the Kleenex of physics.

In a conventional laser you have a laser rod and mirrors. You charge the rod and it starts to emit spontaneous light. That light is reflected from the mirrors and passes through the rod many times, gaining energy from spontaneous emission each time. Eventually you extract the available energy in the rod and a partially coherent beam is emitted from one of the partially transparent mirrors.

Now imagine that rather than use mirrors, you used a lot of rods is series. The effect would be the same, spontaneous em

Very useful post, but it doesn't address my concern. The geometry and coherency are not the issue, it is the stimulated emission. I believe your description of a traditional laser is not quite right: once the initial spontaneous light starts passing through the rod it induces stimulated emission from the other electrons. It is true that mirrors are not necessary, as in the NIF system for example.

As I understand it the electrons going through the undulators are not undergoing stimulated emission, but ar

The original description of a Free Electron Laser by John Madey (in the 70s I think) was entirely quantum-mechanical. This description while correct, is also very complicated (I've been working on FELs on and off since the mid 1980s and I'm afraid all I can do is suggest that you read the papers - I don't understand them). I know that if you look at the electron in the combined field of the undulator and the propagating radiation, a QM description looks just like stimulated emission. I know this is a cop-ou

IANA physicist... I'd like to disagree on the semantics of your point, although you could be right. While the method of stimulation is different from 'traditional' lasers, I would argue that Stimulated Emission of Radiation is still what occurs. I don't see anywhere that requires the population inversion to be a part of the definition - inversion is one of hypothetically many methods. So to my mind, that has only to do with the specific mechanism of lasing, rather than whether it is a laser.

"Stimulated emission" has a specific meaning in physics: an electron (or in theory some other charged particle) is in an excited state, and a photon passing by causes that electron to drop down to a lower energy level and emit a photon of its own. In the case of the FEL we're certainly doing something to the electrons to make them emit photons, but it's not "stimulated emission" in the correct sense.

The nature of stimulated emission is what requires population inversion or somet

Interesting, thanks. So is that why they are tunable? As I understand it, in the 'normal' state, electrons can only emit photons of a certain frequency according to the difference in energy between the excited state and the lower or ground state. So all the light comes out at that frequency. And if I understand what you are saying, the 'wiggler' is shoving the electrons back and forth, and the electrons are emitting energy - as a result of the change in momentum? Or from an interaction between the elec

Since it's xrays, it wouldn't really be Light Amplification anyway but it's hard to pronounce XASER or XRASER. As with many things, the definitions change. LASER (correctly in all caps, rarely done these days) is literally Light Amplification by Stimulated Emission of Radiation (I know you know that!). However, the important aspect is not how it actually works, but the qualities of the EM output. That is coherent and well columnated. So the word laser (as opposed to the acronym LASER) now means a device tha

I have an old (1940's) Microbiology book that mentions a "Proton Microscope" which was evidently invented in France about that time, too.

From what I can tell, they are still sometimes used for metallurgical studies of some kind, but nothing else. I guess although the really small wavelength means you can hypothetically get amazingly high-resolution images, actually getting the beam to focus is extremely technically difficult.

They are not obtaining images but diffraction patterns, which after applying sophisticated methods lets them reconstruct a configuration that is
consistent with the diffraction image, to within some margin of error.
This techniques tend to better for confirming proposed structures that to getting it from scratch.

This has been a bit of a problem. The LCLS is 30X shorter wavelength, and maybe 100X higher power (depending on how you measure) than any previous X-ray laser but its really difficult to describe that without using all sorts of qualifiers. The single shot virus imaging (applicable to a wide range of nanometer scale objects) is far beyond the capabilities of any other system but again the need to apply all sorts of qualifiers makes it sound somewhat weak.